Something I've wondered ever since Halo: Combat
Evolved (SPOILERS!)

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Thanks guys. I never knew they had obtained the "seeds" to repopulate the earth/galaxy/whatever. I don't believe that part was specified in any of the games, but that makes the plot more understandable. Where is the source for this part of the story, btw?

Watch Halo: Legends. It explains it there for sure.

Everyone said it a was a miracle when Jesus hit that grand slam in the bottom of the 9th. I just thought it was a lucky shot.

The plan was to wipe out all life that possessed sentient thought. The Halo pulse ignores most plants, mold, and things like that, and targets brain function. The Halo pulse would kill all the Flood, and render the galaxy incapable of sustaining the Flood if they were to arrive once more from outside the galaxy.

The plan was that the Forerunner fleets and lines of supply could be rebuilt while the Forerunner took use of the breathing room and, once the Flood was confirmed being destroyed and not lurking just beyond the galaxies edge, the life that was extinguished would be reseeded from all the genetic archives they had taken prior to.

Instead, the Flood came too close to winning so they fired it early. Everything died, including the Forerunner. Their automation kept all their stuff in repair, and reseeded all the life samples they harvested from all across the galaxy. Basically restarting everything with little loss of species.

But the Forerunner were never there to ensure the Flood were eliminated and continue guarding the galaxy. So all the species slowly evolved without the Forerunner watching over them, and what little if any info those species remembered became greatly distorted.....aka, the entire Covenant religion.

Pretty much this, the shield world Onyx was a part of the plan to hide sections of space from the Flood